How To Use PubCaseFinder

Overview

Welcome to PubCaseFinder! PubCaseFinder is a web-based clinical decision support system that provides ranked lists of genetic and rare diseases using Human Phenotype Ontology (HPO)-based phenotypic similarities.

Disclaimer

The PubCaseFinder is intended to be used by qualified and licensed physicians to assist in the research about rare and genetic diseases and for use as a teaching aid. The PubCaseFinder should not be used to make medical decisions without the advice of a physician. PubCaseFinder provides data in good faith as a investigative tool, but without verifying the accuracy, clinical validity or utility of the data. In case of commercial use of data, you must refer to the license of the source and confirm the scope of commercial use. PubCaseFinder makes no warranty, express or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used. DBCLS shall bear no liability with respect to damages incurred by the change, discontinuation or termination of the Service.

Beginner's Guide

You can easily check how to use PubCaseFinder on YouTube.

Input

PubCaseFinder provides several functions to help users enter a large number of phenotypes, which facilitate precise patient phenotyping. The text search function enables users to select appropriate phenotypes from the list of hits in a partial match, including synonyms.


Result

A set of phenotypes entered by you can be compared with genetic diseases, rare diseases, causative genes, and open-sharing cases on the basis of phenotypic similarity. A higher phenotypic similarity will show a higher probability for a candidate disease, causative gene, or similar case.


Hierarchical Structure View

The hierarchical structure view function enables you to easily identify higher and lower concept terms of a given phenotype. For example, you can find the phenotype 'microcephaly' by searching its synonym 'small head' and then replace the term with its lower concept 'congenital microcephaly' using the hierarchical structure function.

Filter

The filter function enables you to filter ranked lists in PubCaseFinder to specify a National Center for Biotechnology Information (NCBI) Gene ID as a causative gene, an Human Phenotype Ontology (HPO) term as a mode of inheritance, and/or a Monarch Disease Ontology (Mondo) term as a disease name. When an HPO or Mondo term is specified, all its lower concepts are also subject to the filter. Moreover, this filter supports search expressions using logical operators. For example, when specifying 'autosomal dominant inheritance (HP:0000006),' the ranked list is filtered to 3328 genetic diseases. When specifying 'autoimmune disease (MONDO:0007179),' the list is filtered to 56 genetic diseases. When both 'autosomal dominant inheritance (HP:0000006)' and 'autoimmune disease (MONDO:0007179)' are specified using 'AND' as a logical operator, the ranked list of genetic diseases is filtered to 30.


Download and Share

You can download the result in tsv or json format and get a link to share the result.